Figure 4
From: Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER
Analysis of relative and total sequence weight calculation methods. (A) Local/local mode. (B) Global/local mode. HMMER was run with relative and total sequence weights produced by HMMER or SAM in different combinations. In local/local mode the benefit of SAM's total weight is strong. In global/local mode, the benefit is less pronounced and dependent on using SAM's transition prior. With our implementation of SAM's "bits saved" method for total weight calculation, HMMER performed about as well as using weights estimated by SAM. SAM's recode3.20.comp emission prior was used for all model building.